Mal-ware: Malware is a blanket term to describe any sort of malicious software the intends to harm the user's system

Ad-ware: Adware is often a sponsored installer based addition that is included during a setup process and typically installs some sort of "security protection" or toolbar application.
The "security protection" variants are typically listed as "protect your PC" option during a different program's setup and will usually block installs or uninstalls of future programs.
Another ad-ware approach is the toolbar installs which typically also add an internet browser addon (extension) that sets your default search options and homepage. They also typically pop-up additional windows during internet browsing seemingly at random, but more likely at timed intervals.

Ad-ware is typically fairly straight-forward to uninstall using the control panel's uninstall program section.
It should be noted that if one of these "security protection" variants are installed, they would need to be uninstalled first before any other programs as they typically block the process for other programs.

A computer virus is a form of mal-ware that spreads itself when a program is ran. It will typically copy machine code to other executable files so that the process spreads to other programs.
Another method is to have a program running silently in the background that injects its code into newly run applications. This is not a traditional virus, but most people consider it as such.

A trojan is a metaphor for a virus-type that hides itself as a known executable file such as a program's setup.exe or a common system program such as explorer.exe
These kinds of programs are typically hard to detect as scanning your system for a program listing would let you believe that any running programs are legit.

A keylogger is a type of malware designed to run silently in the background and copy all of your keystrokes to a data file to upload silently in the background on a server, usually foreign.
An example of this was a keylogger that a German teen used to get the security information of Valve's internal networks. He then went on to leak Half-Life 2's source code onto the internet.
He was spared an arrest because of being warned by the German authorities that he was being set-up by Valve and the FBI to visit the U.S.

Worms are typically not used anymore. They are a type of malware that is simply designed to destroy the user's files. They eat their way through file contents by changing them to junk data endlessly.
They were popular when the internet was very new and quickly became unused in favor of more specialized malware.

A common malware practice is to use obfuscation and injection.
Typically in this scenario, a user will make a bit of malware that either has randomized bits, or is mostly random. They then inject their code into a system process such as explorer.exe.
Because these programs are so random, they are typically designed for destruction rather than subterfuge.
This method could be used in conjuction with a keylogger but anything designed to send data over the internet is much easier to notice since people can monitor the network stack.

Successful protection from malware is essentially the same as most medical conditions.
It's far better to prevent them than to try to clean them up after the fact.
This means that you should never allow a website to install any fishy addons and you should definitely not run any executable files.
Forums, comments sections, and security bypassing software - such as keygens, are typically where most of the malware is spread.
They will often rename the exe file to disguise it's intent and make a comment to fool the user to run it.

Back when the internet was newer, people used to spread fake exe files with junk data at the end and pretend they were popular movies.
A little common sense, and knowing to never run any exe file you don't trust will prevent nearly all malware.

There is also Ransom-ware which is a malware designed to hijack the user's sytem until the company gets paid and can give the user a key of sorts to unlock the program.
The user is typically never aware that their system is being ransomed, but instead led to believe that their system is infected with malware and this program is designed to remove it.
A popular method of spreading this type of thing is to put an advertisement on a nefarious website insisting that the user's flash player needs updating. It will then let you download an exe file.
Upon running the exe file, your system is held ransom by a running process that won't let you uninstall it until you've paid and unlocked it.

Really the only professional tools are group policy settings that won't let company users run any elevated programs (Windows is designed to only allow access to system files and registry when running with administrator permission)
Also, a keen eye on a network monitoring program and/or a very efficient hardware-based firewall will weed out most keyloggers; which do the most damage.
Security guards could also block phone and laptop transport and have some sort of electro-static device that would fry any circuitry that personnel would need to pass through.
Someone could limit something like that to a wand type of device similar to airport metal detectors, and wave it over popular hiding spots such as pockets or bras.
The idea behind this is you would fry any microsd or usb flash drive's chipset so that it would need to be professionally repaired to use, if at all.

A company could also buy hardware that has no usb or bluetooth connectivity and instead uses proprietary headset connectivity or add-in cards for conference calls.

Another method of security would be to lock off important data behind passworded encryption barriers.
When I worked at a very large company as a late teen, I know that I had to apply for password permission to literally everything.
This means that a program couldn't simply be hiding in the background, copying these files, as it wouldn't have access.

I honestly wouldn't even recommend sandboxing everything. It's far better to simply never run a suspicious program.
It might not be impossible for someone to code a breakout segment to break out of the sandbox's protections.

Think of it like dealing with a deadly bacteria or something. It's far better to stay away and never touch it, than to put on a suit and risk ripping it or making a foolish mistake.
Plus, what if the thing eats through plastic? Same concept applies with malware. Stay away from suspicious exe files.

That was a bit rambly, but maybe it helped some people get an idea of how to go about security.
The last thing you would ever want to do is install anti-virus program and just think you're secure and able to run anything.
Malware is designed to bypass detection; that's why it's so successful.

can't wait to see the finished product. hope all counter measures are going to be discussed ( i.e. firewalls, proxies, vpns, ) the list can go on and on. only problem is everyone is going to post i use this or i use that without giving a solid reason why, what version ( security varies with version ), what OS, is the product freeware, adware ( lol ), or do you have to pay for it. also a lot of security solutions are installed by people who don't even go into the settings and dig in to find out what's going on inside. if you use the default settings in a lot of programs it slows the hell out of your computer, what tweaks can be made without compromising security.
anyways, can't wait for this, and thanks for this herculean effort. bookmarked to see how it develops.